fix restart file writing when grid has no y-guard cells

xbout/calc/turbulence.py

@@ -1,7 +1,6 @@
 import numpy as np
 import xarray as xr
 
-
 # TODO write a decorator to add functions as accessors to dataarrays?
 
 

xbout/conftest.py

@@ -1,6 +1,5 @@
 import pytest
 
-
 configure_is_imported = False
 
 

xbout/geometries.py

@@ -60,13 +60,9 @@ def apply_geometry(ds, geometry_name, *, coordinates=None, grid=None):
         try:
             add_geometry_coords = REGISTERED_GEOMETRIES[geometry_name]
         except KeyError:
-            message = dedent(
-                """{} is not a registered geometry. Inspect the global
+            message = dedent("""{} is not a registered geometry. Inspect the global
                              variable REGISTERED_GEOMETRIES to see which geometries
-                             have been registered.""".format(
-                    geometry_name
-                )
-            )
+                             have been registered.""".format(geometry_name))
             raise UnregisteredGeometryError(message)
 
         # User-registered functions may accept 'coordinates' and 'grid' arguments, but

xbout/plotting/animate.py

@@ -14,7 +14,6 @@
 )
 from matplotlib.animation import PillowWriter
 
-
 if (
     "pcolor.shading" in matplotlib.rcParams
     and matplotlib.rcParams["pcolor.shading"] == "flat"

xbout/plotting/plotfuncs.py

@@ -18,7 +18,6 @@
     plot_targets,
 )
 
-
 if (
     "pcolor.shading" in matplotlib.rcParams
     and matplotlib.rcParams["pcolor.shading"] == "flat"

xbout/tests/test_boutdataset.py

@@ -20,7 +20,6 @@
 from xbout.utils import _set_attrs_on_all_vars, _1d_coord_from_spacing
 from xbout.tests.utils_for_tests import set_geometry_from_input_file
 
-
 EXAMPLE_OPTIONS_FILE_PATH = "./xbout/tests/data/options/BOUT.inp"
 
 

xbout/tests/test_region.py

@@ -6,7 +6,6 @@
 
 from xbout import open_boutdataset
 
-
 params_guards = "guards"
 params_guards_values = [
     pytest.param({"x": 0, "y": 0}, marks=pytest.mark.long),

xbout/tests/utils_for_tests.py

@@ -6,7 +6,6 @@
 from pathlib import Path
 from xarray import DataArray, Dataset
 
-
 # Note, MYPE, PE_XIND and PE_YIND not included, since they are different for each
 # processor and so are dropped when loading datasets.
 METADATA_VARS = [

xbout/utils.py

@@ -324,7 +324,11 @@ def _pad_y_boundaries(ds):
     ycoord = ds.metadata.get("bout_ydim", "y")
     has_second_divertor = ds.metadata["jyseps2_1"] != ds.metadata["jyseps1_2"]
 
-    if not ds.metadata["keep_yboundaries"] and myg > 0:
+    if (
+        not ds.metadata["keep_yboundaries"]
+        and myg > 0
+        and ds.metadata["ny"] == ds.dims["y"]
+    ):
         boundary_pad = ds.isel({ycoord: slice(myg)}).copy(deep=True).load()
         for v in boundary_pad:
             if ycoord in boundary_pad[v].dims: